Life in changing environments

Abstract

Cells are complex systems continuously exposed to changing, dynamic environments. Understanding how cells respond and adapt is of great interest not only from a fundamental viewpoint but also for the development of solutions for current challenges in medical, industrial and environmental research fields.

In this thesis, the bacterial community member Candidatus Accumulibacter phosphatis (hereafter referred to as Accumulibacter) from the functional group of Polyphosphate Accumulating Organisms (PAOs) was selected as study object due to their key-role in phosphorus removal at wastewater treatment processes and their adaptive metabolic strategies to thrive in fluctuating environments. These microorganisms are enriched in Enhanced Biological Phosphorus removal (EBPR) systems where they experience cyclic absence and presence of external electron acceptors (here, anaerobic and aerobic conditions, respectively). These fluctuations together with non-continuous availability of nutrients lead to intricate metabolic strategies. While the overall metabolic traits of these bacteria are well described, the non-availability of isolates has led to controversial hypotheses on which metabolic pathways are used - structure, when are these pathways active - function, and what mechanisms control the operation of these pathways - regulation. These hypotheses were further analysed and discussed in this dissertation.

While the bacterial community member Accumulibacter was the cellular system example studied here, this doctoral dissertation explored and combined systems biology methods to improve the mechanistic understanding of cells as structured metabolic systems with functional and regulatory frameworks, which respond and adapt to changing external conditions (environments). The developed and applied approaches are not only specific to Accumulibacter and can be applied to other cell systems and communities exposed to changing environments.